Based on your pKa prediction by PDB2PQR, set protonation state for
Asp/Glu/His/Lys/Arg accordingly. That is all you can do in GROMACS.
Constant pH MD should be used if you want to make your simulation pH
responsive.
Cheers
On Wed, May 17, 2017 at 11:18 AM, ZHANG Cheng <272699...@qq.com> wrote:
> Dear Gromacs,I am simulating pH 4 condition. I interactively assign the
> protonation of chargeable residues of a protein based on PDB2PQR results by
> setting pH=4 in the "pKa Options" (http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/
> ).
>
>
> I do not add citrate or acetate molecules to the simulation box. So if the
> pH 4 condition could still be reflected?
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng
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--
*Zhi Yue*
Graduate Research Assistant
Computer-Aided Drug Design Center
School of Pharmacy
University of Maryland
20 Penn St, Rm S612
Baltimore, MD 21201-1075
Email:zhi...@umaryland.edu
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